Created
November 29, 2012 16:50
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run patscan (to search for a pattern) on every sequence in a directory
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#!/usr/bin/perl -w | |
# patscan_batch.pl | |
# Run patscan on all seqs in a folder | |
# Can be easily modified to run any command on every sequence in a folder | |
# WI Bioinformatics course - Feb 2002 - Lecture 5 | |
# Revised - Sep 2003 | |
################ User-supplied variables ############# | |
# Directory of sequences | |
$myDir = "/home/elvis/seqs"; | |
# Output directory (relative to $myDir or full path) | |
$outputDir = "patscan"; | |
# Path to pattern file | |
$patFile = "/home/elvis/patterns/polyA.pat"; | |
######################################################### | |
# Go to sequence directory and open it (i.e, read contents) | |
chdir($myDir) || die "Cannot change to $myDir: $!"; # Go to $myDir | |
opendir(DIR, $myDir) || die "Cannot open $myDir: $!"; # Open $myDir | |
foreach $seqFile (sort readdir(DIR)) | |
{ | |
if ($seqFile =~ /\.tfa$/) # if file ends in .tfa | |
{ | |
print "Processing $seqFile\n"; | |
$outFile = $seqFile; # Create $outFile name | |
$outFile =~ s/\.tfa/\.polyA\.out/; # s/old/new/; | |
############ Run PATSCAN ############### | |
`scan_for_matches $patFile < $seqFile > $outputDir/$outFile`; | |
} | |
} | |
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